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Belgingur / WrfUtils

Utilities for working with wrfout files.
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DropDigits writes empty netCDF file if sigma_limit is set #21

Closed olafurrognvaldsson closed 4 years ago

olafurrognvaldsson commented 4 years ago

DropDigits writes no values in the new netCDF file when used with sigma_limit = xx

logi commented 4 years ago

I am unable to reproduce this issue. If I uncomment the sigma_limit: 5 line from DropDigits.yml and run against the 1.4G file from #20 (downloader@binary.belgingur.is:wod_test_data/jobs/2016/10/20161024-africa-50/model/wrfout_d01_2016-10-24_06:00:00) then I get this written to console:

(DropDigits) logi@saxi:~/belgingur.is/WrfUtils.git/DropDigits$ ./DropDigits.py /home/logi/wod_test_data/jobs/2016/10/20161024-africa-50/model/wrfout_d01_2016-10-24_06:00:00
2020-01-15 17:05:16 |    INFO | Configured logging from /home/logi/belgingur.is/WrfUtils.git/DropDigits/logging.yml
2020-01-15 17:05:16 |    INFO | Load config from DropDigits.yml
2020-01-15 17:05:16 |    INFO | 
2020-01-15 17:05:16 |    INFO | Opening input dataset /home/logi/wod_test_data/jobs/2016/10/20161024-africa-50/model/wrfout_d01_2016-10-24_06:00:00
2020-01-15 17:05:16 |    INFO | Include all variables except []
2020-01-15 17:05:16 |    INFO | Excluded variables: <none>
2020-01-15 17:05:16 |    INFO | Included variables: Times, XLAT, XLONG, U, V, W, PH, PHB, T, TKE, P, ALT, PB, Q2, T2, PSFC, U10, V10, ITIMESTEP, RELHUM, RH2, MSLP, QVAPOR, QCLOUD, QRAIN, TSLB, SMOIS, GRDFLX, ACSNOM, SNOW, SNOWH, TKE_PBL, SINALPHA, COSALPHA, HGT, RAINC, RAINNC, SWDOWN, GLW, XLAT_U, XLONG_U, XLAT_V, XLONG_V, PBLH, REGIME, SNOWC, SR, BN2, SAVE_TOPO_FROM_REAL, SEED1, SEED2, LAKEMASK, SST
2020-01-15 17:05:16 |    INFO | Dimensional limits
2020-01-15 17:05:16 |    INFO |     Spinup is 0h = 0 steps
2020-01-15 17:05:16 |    INFO |     Margin is 10 cells
2020-01-15 17:05:17 |    INFO |     3D variables limited to 5 levels which reach at least 309m above sea level and 309m above surface level
2020-01-15 17:05:17 |    INFO | Creating output file ./wrfout_d01_2016-10-24_06:00:00_reduced.nc
2020-01-15 17:05:17 |    INFO | Setting/updating global file attributes for output file
2020-01-15 17:05:17 |    INFO | Copy 114 attributes
2020-01-15 17:05:17 |    INFO | Add attributes:
2020-01-15 17:05:17 |    INFO |     history = Converted with DropDigits.py at 2020-05-15 17:01:17 by logi on saxi
2020-01-15 17:05:17 |    INFO |     source = /home/logi/wod_test_data/jobs/2016/10/20161024-africa-50/model/wrfout_d01_2016-10-24_06:00:00
2020-01-15 17:05:17 |    INFO |     institution = Belgingur
2020-01-15 17:05:17 |    INFO |     description = Reduced version of: /home/logi/wod_test_data/jobs/2016/10/20161024-africa-50/model/wrfout_d01_2016-10-24_06:00:00
2020-01-15 17:05:17 |    INFO | Add output dimensions:
2020-01-15 17:05:17 |    INFO |     Time (28)
2020-01-15 17:05:17 |    INFO |     DateStrLen (19)
2020-01-15 17:05:17 |    INFO |     west_east (164)
2020-01-15 17:05:17 |    INFO |     south_north (179)
2020-01-15 17:05:17 |    INFO |     west_east_stag (165)
2020-01-15 17:05:17 |    INFO |     bottom_top (5)
2020-01-15 17:05:17 |    INFO |     south_north_stag (180)
2020-01-15 17:05:17 |    INFO |     bottom_top_stag (6)
2020-01-15 17:05:17 |    INFO |     soil_layers_stag (4)
2020-01-15 17:05:17 |    INFO | Excluded dimensions: <none>
2020-01-15 17:05:17 |    INFO | Create output variables with overrides:
2020-01-15 17:05:17 |    INFO |     Times      |S1        None … None [Time,DateStrLen]
2020-01-15 17:05:17 |    INFO |     XLAT       f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     XLONG      f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     U          i2*0.01    -327.68 … 327.67 [Time,bottom_top,south_north,west_east_stag]
2020-01-15 17:05:17 |    INFO |     V          i2*0.01    -327.68 … 327.67 [Time,bottom_top,south_north_stag,west_east]
2020-01-15 17:05:17 |    INFO |     W          i2*0.01    -327.68 … 327.67 [Time,bottom_top_stag,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     PH         f4         -3.4e+38 … 3.4e+38 [Time,bottom_top_stag,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     PHB        f4         -3.4e+38 … 3.4e+38 [Time,bottom_top_stag,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     T          i2*0.01    -327.68 … 327.67 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     TKE        i2*0.001-32.768 0.0 … 65.535 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     P          i2*0.2     -6553.6 … 6553.400000000001 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     ALT        i2*0.001-32.768 0.0 … 65.535 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     PB         i2*2-65536 0 … 131070 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     Q2         f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     T2         i2*0.01-327.68 0.0 … 655.35 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     PSFC       i2*2-65536 0 … 131070 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     U10        i2*0.01    -327.68 … 327.67 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     V10        i2*0.01    -327.68 … 327.67 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     ITIMESTEP  i4         -2147483648 … 2147483647 [Time]
2020-01-15 17:05:17 |    INFO |     RELHUM     i2*0.01-327.68 0.0 … 655.35 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     RH2        i2*0.01-327.68 0.0 … 655.35 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     MSLP       i2*2-65536 0 … 131070 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     QVAPOR     i2*8e-06-0.0262144 -0.2359296 … 0.2883504 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     QCLOUD     i2*8e-06-0.0262144 -0.2359296 … 0.2883504 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     QRAIN      i2*8e-06-0.0262144 -0.2359296 … 0.2883504 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     TSLB       i2*0.01-327.68 0.0 … 655.35 [Time,soil_layers_stag,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SMOIS      i2*0.0001-3.2768 0.0 … 6.5535 [Time,soil_layers_stag,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     GRDFLX     i2*0.1     -3276.8 … 3276.7000000000003 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     ACSNOM     i2*0.1-3276.8 0.0 … 6553.5 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SNOW       f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SNOWH      i2*0.001-32.768 0.0 … 65.535 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     TKE_PBL    i2*0.001-32.768 0.0 … 65.535 [Time,bottom_top_stag,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SINALPHA   i2*0.0001  -3.2768 … 3.2767 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     COSALPHA   i2*0.0001-3.2768 0.0 … 6.5535 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     HGT        i2*0.2-4000 -2553.6000000000004 … 10553.400000000001 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     RAINC      f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     RAINNC     f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SWDOWN     i2*0.1-3276.8 0.0 … 6553.5 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     GLW        i2*0.01-327.68 0.0 … 655.35 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     XLAT_U     f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east_stag]
2020-01-15 17:05:17 |    INFO |     XLONG_U    f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east_stag]
2020-01-15 17:05:17 |    INFO |     XLAT_V     f4         -3.4e+38 … 3.4e+38 [Time,south_north_stag,west_east]
2020-01-15 17:05:17 |    INFO |     XLONG_V    f4         -3.4e+38 … 3.4e+38 [Time,south_north_stag,west_east]
2020-01-15 17:05:17 |    INFO |     PBLH       f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     REGIME     i1         -128 … 127 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SNOWC      i1         -128 … 127 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SR         i1*0.01    -1.28 … 1.27 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     BN2        i2*1e-06   -0.032768 … 0.032767 [Time,bottom_top,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SAVE_TOPO_FROM_REAL i2*0.0001-3.2768 0.0 … 6.5535 [Time]
2020-01-15 17:05:17 |    INFO |     SEED1      i2*0.0001-3.2768 0.0 … 6.5535 [Time]
2020-01-15 17:05:17 |    INFO |     SEED2      i2*0.0001-3.2768 0.0 … 6.5535 [Time]
2020-01-15 17:05:17 |    INFO |     LAKEMASK   f4         -3.4e+38 … 3.4e+38 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO |     SST        i2*0.01-327.68 0.0 … 655.35 [Time,south_north,west_east]
2020-01-15 17:05:17 |    INFO | Copying data in chunks of 128 time steps
2020-01-15 17:05:17 |    INFO | Chunk[0:28]: 2016-10-24 06:00:00 - 2016-10-25 09:00:00
2020-01-15 17:05:17 |    INFO |     Variable            Min          Max
2020-01-15 17:05:17 |    INFO |     Times               N/A          N/A
2020-01-15 17:05:17 |    INFO |     XLAT             -36.32        37.91
2020-01-15 17:05:18 |    INFO |     XLONG            -21.65        51.65
2020-01-15 17:05:19 |    INFO |     U                -25.28        22.67
2020-01-15 17:05:20 |    INFO |     V                -25.06        36.79
2020-01-15 17:05:21 |    INFO |     W                 -0.68         0.36
2020-01-15 17:05:23 |    INFO |     PH              -116.28       491.29
2020-01-15 17:05:24 |    INFO |     PHB           -1,414.61    32,060.61
2020-01-15 17:05:25 |    INFO |     T                -18.88        22.09
2020-01-15 17:05:25 |    INFO |     TKE                0.00         0.00
2020-01-15 17:05:26 |    INFO |     P               -689.10     2,952.23
2020-01-15 17:05:27 |    INFO |     ALT                0.80         1.19
2020-01-15 17:05:28 |    INFO |     PB            67,634.44   101,373.15
2020-01-15 17:05:28 |    INFO |     Q2                 0.00         0.03
2020-01-15 17:05:28 |    INFO |     T2               272.67       314.89
2020-01-15 17:05:28 |    INFO |     PSFC          72,961.61   104,602.08
2020-01-15 17:05:28 |    INFO |     U10              -15.94        16.04
2020-01-15 17:05:29 |    INFO |     V10              -17.36        19.75
2020-01-15 17:05:29 |    INFO |     ITIMESTEP          0.00       397.00
2020-01-15 17:05:30 |    INFO |     RELHUM             2.89       100.00
2020-01-15 17:05:30 |    INFO |     RH2                6.57       100.00
2020-01-15 17:05:30 |    INFO |     MSLP          99,311.56   102,925.48
2020-01-15 17:05:31 |    INFO |     QVAPOR             0.00         0.02
2020-01-15 17:05:32 |    INFO |     QCLOUD             0.00         0.00
2020-01-15 17:05:32 |    INFO |     QRAIN              0.00         0.00
2020-01-15 17:05:33 |    INFO |     TSLB             273.16       318.79
2020-01-15 17:05:33 |    INFO |     SMOIS              0.02         1.00
2020-01-15 17:05:33 |    INFO |     GRDFLX          -344.14       141.04
2020-01-15 17:05:33 |    INFO |     ACSNOM             0.00         0.80
2020-01-15 17:05:33 |    INFO |     SNOW               0.00         8.05
2020-01-15 17:05:33 |    INFO |     SNOWH              0.00         0.05
2020-01-15 17:05:34 |    INFO |     TKE_PBL            0.10         5.60
2020-01-15 17:05:34 |    INFO |     SINALPHA          -0.00        -0.00
2020-01-15 17:05:34 |    INFO |     COSALPHA           1.00         1.00
2020-01-15 17:05:34 |    INFO |     HGT             -144.20     2,788.55
2020-01-15 17:05:34 |    INFO |     RAINC              0.00        67.00
2020-01-15 17:05:34 |    INFO |     RAINNC            -0.00        78.88
2020-01-15 17:05:34 |    INFO |     SWDOWN             0.00     1,162.79
2020-01-15 17:05:34 |    INFO |     GLW                0.00       478.03
2020-01-15 17:05:34 |    INFO |     XLAT_U           -36.32        37.91
2020-01-15 17:05:34 |    INFO |     XLONG_U          -21.88        51.88
2020-01-15 17:05:34 |    INFO |     XLAT_V           -36.50        38.09
2020-01-15 17:05:34 |    INFO |     XLONG_V          -21.65        51.65
2020-01-15 17:05:35 |    INFO |     PBLH               0.00     5,478.49
2020-01-15 17:05:35 |    INFO |     REGIME             0.00         0.00
2020-01-15 17:05:35 |    INFO |     SNOWC              0.00         0.42
2020-01-15 17:05:35 |    INFO |     SR                -0.35         1.00
2020-01-15 17:05:36 |    INFO |     BN2               -0.00         0.01
2020-01-15 17:05:36 |    INFO |     SAVE_TOPO_FROM_REAL         0.00         0.00
2020-01-15 17:05:36 |    INFO |     SEED1              0.00         0.00
2020-01-15 17:05:36 |    INFO |     SEED2              0.00         0.00
2020-01-15 17:05:36 |    INFO |     LAKEMASK           0.00         0.00
2020-01-15 17:05:36 |    INFO |     SST              267.71       337.07
2020-01-15 17:05:36 |    INFO | Size: 1,385,386 MB -> 76,262 MB, reduced to 5.5% in 20.5 s

And the beginning of ncdump looks like this:

netcdf wrfout_d01_2016-10-24_06\:00\:00_reduced {
dimensions:
        Time = 28 ;
        DateStrLen = 19 ;
        west_east = 164 ;
        south_north = 179 ;
        west_east_stag = 165 ;
        bottom_top = 5 ;
        south_north_stag = 180 ;
        bottom_top_stag = 6 ;
        soil_layers_stag = 4 ;

@olafurrognvaldsson can you show me output from a failing run and perhaps even a config and data file that fails to run?

olafurrognvaldsson commented 4 years ago

What happens if you do e.g. ncdump -v T2 wrfout_d01_2016-10-24_06\:00\:00_reduced?

logi commented 4 years ago 
...
        :source = "/home/logi/wod_test_data/jobs/2016/10/20161024-africa-50/model/wrfout_d01_2016-10-24_06:00:00" ;
        :institution = "Belgingur" ;
        :description = "Reduced version of: /home/logi/wod_test_data/jobs/2016/10/20161024-africa-50/model/wrfout_d01_2016-10-24_06:00:00" ;
data:

 T2 =
  -3974, -3977, -3963, -3953, -3954, -3966, -3979, -3991, -3999, -3995,
    -3988, -3981, -3979, -3997, -4027, -4045, -4063, -4072, -4076, -4070,
    -4062, -4061, -4072, -4082, -4096, -4129, -4142, -4114, -4083, -4069,
    -4073, -4104, -4122, -4118, -4103, -4067, -4019, -3975, -3943, -3919,
    -3899, -3882, -3864, -3847, -3832, -3828, -3841, -3872, -3899, -3920,
    -3949, -3973, -4000, -4031, -4065, -4096, -4118, -4120, -4122, -4119,
    -4114, -4106, -4097, -4086, -4075, -4058, -4038, -4020, -4006, -3995,
    -3972, -3958, -3962, -3967, -3966, -3950, -3932, -3906, -3879, -3854,
    -3824, -3790, -3761, -3747, -3754, -3765, -3778, -3783, -3776, -3768,
    -3753, -3732, -3711, -3695, -3684, -3671, -3641, -3578, -3504, -3475,
    -3475, -3487, -3504, -3531, -3565, -3589, -3585, -3584, -3601, -3627,
    -3652, -3668, -3681, -3689, -3688, -3683, -3680, -3675, -3667, -3661,
    -3657, -3654, -3649, -3652, -3654, -3659, -3660, -3664, -3676, -3696,
    -3707, -3706, -3709, -3711, -3706, -3705, -3713, -3719, -3712, -3709,
    -3712, -3716, -3713, -3702, -3686, -3677, -3672, -3674, -3666, -3666,
    -3661, -3661, -3675, -3669, -3652, -3650, -3669, -3677, -3690, -3705,
    -3713, -3729, -3732, -3740,
  -3969, -3975, -3969, -3966, -3963, -3967, -3977, -3986, -3987, -3974,
    -3959, -3952, -3954, -3974, -4005, -4027, -4053, -4067, -4068, -4063,
    -4057, -4054, -4062, -4070, -4077, -4094, -4096, -4074, -4046, -4036,
    -4044, -4067, -4060, -4020, -3989, -3953, -3914, -3899, -3884, -3867,
...
olafurrognvaldsson commented 4 years ago

Interesting, try changing the sign in the yml-file so it reads add_offset: 327.68 for variable T2 (these are some mighty low values ... :)

logi commented 4 years ago

That sounds like a completely separate issue?

olafurrognvaldsson commented 4 years ago

The shit gets faunkier. When I run this here

#!/bin/bash
#
source _python_env_
# 
for i in `ls /riv/scrooge/RAV2/2018-19/wrfout_d01_2018-08-25*`
do
  echo "/home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py " $i
  /home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py $i
done

I get this error message

2020-01-15 20:08:16 |   ERROR | Uncaught exception in main()
Traceback (most recent call last):
  File "/home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py", line 486, in <module>
    main()
  File "/home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py", line 309, in main
    errors = process_file(in_file, out_file, config=config, overrides=overrides)
  File "/home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py", line 438, in process_file
    in_chunk: np.ndarray = in_var[c_start:c_end, 0:var_max_k, margin:max_j - margin, margin:max_i - margin]
  File "netCDF4/_netCDF4.pyx", line 4095, in netCDF4._netCDF4.Variable.__getitem__
  File "/home/or/miniconda3/envs/DropDigits/lib/python3.7/site-packages/netCDF4/utils.py", line 330, in _StartCountStride
    raise ValueError("slicing expression exceeds the number of dimensions of the variable")
ValueError: slicing expression exceeds the number of dimensions of the variable
Traceback (most recent call last):
  File "/home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py", line 486, in <module>
    main()
  File "/home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py", line 309, in main
    errors = process_file(in_file, out_file, config=config, overrides=overrides)
  File "/home/or/Belgingur-Utils-20191227/WrfUtils/DropDigits/DropDigits.py", line 438, in process_file
    in_chunk: np.ndarray = in_var[c_start:c_end, 0:var_max_k, margin:max_j - margin, margin:max_i - margin]
  File "netCDF4/_netCDF4.pyx", line 4095, in netCDF4._netCDF4.Variable.__getitem__
  File "/home/or/miniconda3/envs/DropDigits/lib/python3.7/site-packages/netCDF4/utils.py", line 330, in _StartCountStride
    raise ValueError("slicing expression exceeds the number of dimensions of the variable")
ValueError: slicing expression exceeds the number of dimensions of the variable

But now I'm not going to stare at this longer tonight

logi commented 4 years ago

I need more of the output. That doesn't give any indication which variable it is failing on or which variables succeeded.

logi commented 4 years ago

@olafurrognvaldsson Can you please trigger the error by running DropDigits on exactly one netCDF file with the new --verbose flag and attach both the full console output to this issue along with the config file used and the path of the netCDF file. That should isolate the problem.

olafurrognvaldsson commented 4 years ago

DropDigits.yml.log DropDigits.sh.log dropdigits.log

The error appears when the code tries to process the variable float ZNU(Time, bottom_top)

The way the code is run is shown in DropDigits.sh.log (I can't upload files ending in .sh or .yml, hence the extra ".log").

logi commented 4 years ago

OK, and the way that ZNU and ZNW are different from other variables I've seen is that they have a vertical dimension but no planar dimensions:

2020-01-16 12:32:52 |    INFO |     ZNU        i2*0.0001-3.2768 0.0 … 6.5535 [Time,bottom_top]
2020-01-16 12:32:52 |    INFO |     ZNW        i2*0.0001-3.2768 0.0 … 6.5535 [Time,bottom_top_stag]

and

<class 'netCDF4._netCDF4.Variable'>
int16 ZNU(Time, bottom_top)
    description: eta values on half (mass) levels
    least_significant_digit: 4
    scale_factor: 0.0001
    add_offset: -3.2768
    FieldType: 104
    MemoryOrder: Z  
    units: 
    stagger: 
unlimited dimensions: 
current shape = (56, 5)
filling on, default _FillValue of -32767 used

<class 'netCDF4._netCDF4.Variable'>
int16 ZNW(Time, bottom_top_stag)
    description: eta values on full (w) levels
    least_significant_digit: 4
    scale_factor: 0.0001
    add_offset: -3.2768
    FieldType: 104
    MemoryOrder: Z  
    units: 
    stagger: Z
unlimited dimensions: 
current shape = (56, 6)
filling on, default _FillValue of -32767 used

while the code assumes that if there is a vertical dimension that needs to be sliced then there will be planar dimensions as well. This is something I can fix:

2020-01-16 12:32:54 |   DEBUG | var_name: ZNU
2020-01-16 12:32:54 |   DEBUG | in_var.shape: (56, 64)
2020-01-16 12:32:54 |   DEBUG | in_slice: [0:56,0:5,10:46,10:54]

should be:

2020-01-16 12:32:54 |   DEBUG | var_name: ZNU
2020-01-16 12:32:54 |   DEBUG | in_var.shape: (56, 64)
2020-01-16 12:32:54 |   DEBUG | in_slice: [0:56,0:5]
logi commented 4 years ago

@olafurrognvaldsson Try it again please?

olafurrognvaldsson commented 4 years ago

@logi works like a charm !!

logi commented 4 years ago

There is still an assumption in the code that if there is one planar dimension (staggered or not) exactly when the other planar dimension is present (independently staggered or not).